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Sample GSM2897330 Query DataSets for GSM2897330
Status Public on Dec 21, 2020
Title THP-1 macrophages stimulated with nBSA for 24 hours
Sample type SRA
 
Source name THP-1 macrophages
Organism Homo sapiens
Characteristics cell type: THP-1 macrophages
agent: nBSA
time point: 24 hours
Treatment protocol THP-1 macrophages were stimulated in triplicates with 0.8 µg/ml nESAT6 (ESAT6 purchased from Catlog No. ab124574, Abcam, USA) or 0.8 µg/ml nBSA for 4 h or 24 h. Cells were placed in a humidified, 37℃ 5% CO2 incubator.
Growth protocol Human monocyte cell line THP-1 was cultured in RPMI 1640 basic medium (Gibco, life technologies, USA) supplemented with 2 mM L-glutamine, Penicillin (100 U/ml)-Streptomycin (100 µg/ml) Solution and 10% fetal bovine serum (FBS) (Catalog No. 04-121-1A, Biological Industries, Israel) at cultural density of 5 × 105 - 1 × 106/ml.
Extracted molecule total RNA
Extraction protocol The total RNA were isolated with RNeasy mini kit (Qiagen, Germany) according to the manufacturer's instructions
The libraries were prepared with KAPA Stranded mRNA-Seq Kit for Illumina (Kapa biosystems, USA) following the manufacturer's procedure. In Brief, high quality intact total RNA (200 ng in 50 µl RNase-free water) were input for Poly(A) RNA capture with magnetic oligo-dT beads. The RNA was fragmented to the desired size (about 300 bp) by heating in the presence of Mg++. The 1st strand cDNA was synthesized with random primers. The 2nd strand cDNA synthesis converted cDNA:RNA hybrid to double strand cDNA (dscDNA), while marking the 2nd strand with dUTP. Then dAMP was added to 3’-end of dscDNA fragments. Following by ligation of 3’-dTMP adapters (10 nM) to 3’-dAMP library fragments, and PCR amplification (14 cycles) of the adapter-ligated library DNA. The dUTP-marked strand was not amplified. Library fragment size distribution was confirmed by electrophoresis and library concentration was determined with Qubit 2.0 Fluorometric Quantitation (Thermo Fisher Scientific, USA). These libraries were sequenced using the Illumina Hiseq 3000 Sequencer (50 cycles, single read lane).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description nBSA_24h
Data processing Quality control analysis of the raw sequence files was conducted with FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The quality-checked reads for each condition were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0)
Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15) and normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample ...
 
Submission date Dec 21, 2017
Last update date Dec 21, 2020
Contact name Fake Li
E-mail(s) cqlfk@hotmail.com
Phone 8613677631560
Organization name Daping Hospital
Department Clinical Laboratory Medicine
Lab Gezhi Lab
Street address Changjiangzhilu 10 Yuzhong District
City Chongqing
State/province Chongqing
ZIP/Postal code 400042
Country China
 
Platform ID GPL21290
Series (1)
GSE108393 RNA-seq identifies a distinct response in macrophages stimulated from phagosome with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis
Relations
BioSample SAMN08223906
SRA SRX3502539

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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